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- PDB-8pqt: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pqt | ||||||
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Title | Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to Bis-Tris | ||||||
![]() | Nucleoside 2-deoxyribosyltransferase | ||||||
![]() | TRANSFERASE / Bis-Tris / WT | ||||||
Function / homology | deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / Nucleoside 2-deoxyribosyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tang, P. / Harding, C.J. / Czekster, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase. Authors: Tang, P. / Harding, C.J. / Dickson, A.L. / da Silva, R.G. / Harrison, D.J. / Czekster, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.4 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pqpC ![]() 8pqqC ![]() 8pqrC ![]() 8pqsC ![]() 8qc0C ![]() 8rh3C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17689.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7203 / Gene: Chro_1188 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.03 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 9.8 mg/ml enzyme; 22.5% v/v PEG Smear Broad; 0.1 M Bis-Tris pH 7.5; 0.05 M Zinc acetate dihydrate; 0.2 M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→113.61 Å / Num. obs: 48818 / % possible obs: 100 % / Redundancy: 50.9 % / CC1/2: 1 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.02 / Rrim(I) all: 0.146 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 29.5 % / Rmerge(I) obs: 1.626 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2409 / CC1/2: 0.955 / Rpim(I) all: 0.299 / Rrim(I) all: 1.654 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→69.04 Å
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Refine LS restraints |
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LS refinement shell |
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